Sun Oct 9 15:10:54 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 15:10:54 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5362 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.5163386 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -16.08500 52.86200 ymin,ymax (A): 98.54200 167.0460 zmin,zma (A): -29.86400 31.83100 x,y,z range (A): 68.94701 68.50401 61.69500 scale (grids/A): 0.5163386 object centre (A): 18.38850 132.7940 0.9835005 number of atom coordinates read : 5362 total number of charged atoms : 5190 net assigned charge : -5.499956 assigned positive charge : 818.3576 centred at (gu) : 89.29791 88.52393 88.15302 assigned negative charge : -823.8639 centred at (gu) : 89.27838 88.61170 88.09307 start vw surface at 0.2400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 8879 nv = 96 ne = 84 npr = 110364 no. pairs analyzed = 110364 no. exposed pairs = 6151 no. arc points = 42537 no. surface atoms = 2078 nbur = 3284 mkacc time = 0.3600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 296 mr = 4905 m= 0 mr = 5 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.7000000 number of dielectric boundary points 4265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4125 ## 553 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 11853 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3537363E-10 7.5859159E-11 midg,1,midg; midg,igrid,midg 3.4148545E-10 -2.9699651E-10 1,midg,midg; igrid,midg,midg -2.0871066E-10 -2.2410256E-11 gauss-seidel spectral radius is 0.9808449 estimated iterations to convergence 60 setup time was (sec) 1.020000 now iterating at: 15:10:55 rms-change max change #iterations 7.5977892E-02 10.52511 at 10iterations 6.1049936E-03 0.8493385 at 20iterations 1.2749488E-03 0.2280006 at 30iterations 3.6710844E-04 6.6591263E-02 at 40iterations 1.0724301E-04 1.9449234E-02 at 50iterations finished qdiffx linear iterations at : 15:10:59 total time elapsed so far: 4.760000 # loops : 50 mean,max change (kT/e) : 1.0724301E-04 1.9449234E-02 energy calculations done at 4.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.970000 DelPhi exited at 15:11:00 4.977u 0.444s 0:05.69 95.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 15:11:00 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5362 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.549016 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -16.08500 52.86200 ymin,ymax (A): 98.54200 167.0460 zmin,zma (A): -29.86400 31.83100 x,y,z range (A): 68.94701 68.50401 61.69500 scale (grids/A): 1.549016 object centre (A): 18.38850 132.7940 0.9835005 number of atom coordinates read : 5362 total number of charged atoms : 5190 net assigned charge : -5.499956 assigned positive charge : 818.3576 centred at (gu) : 87.89199 85.57031 84.45782 assigned negative charge : -823.8639 centred at (gu) : 87.83502 85.83493 84.27888 start vw surface at 0.2400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 100653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42537 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29397 mr = 71801 m= 2562 mr = 20197 m= 47 mr = 1116 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 3476 time to turn everything in is 1.010000 number of dielectric boundary points 39545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 503 ## 7 charges are in solution ## iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 39086 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5163386 object centre at (A) : 18.38850 132.7940 0.9835005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3475777E-03 -6.6873604E-03 midg,1,midg; midg,igrid,midg 2.4246139E-02 -1.7054632E-02 1,midg,midg; igrid,midg,midg -2.8170465E-02 7.5455516E-04 gauss-seidel spectral radius is 0.9981878 estimated iterations to convergence 187 setup time was (sec) 1.350000 now iterating at: 15:11:01 rms-change max change #iterations 4.190829 205.2044 at 10iterations 1.748640 52.82795 at 20iterations 0.7326976 21.65188 at 30iterations 0.3070607 10.52549 at 40iterations 0.1284090 3.776867 at 50iterations 5.3884964E-02 1.647179 at 60iterations 2.2762755E-02 0.6767883 at 70iterations 9.7097829E-03 0.2865582 at 80iterations 4.1970662E-03 0.1382771 at 90iterations 1.8880065E-03 6.3785553E-02 at 100iterations 8.9356187E-04 3.0403137E-02 at 110iterations 4.5557137E-04 1.7490387E-02 at 120iterations finished qdiffx linear iterations at : 15:11:11 total time elapsed so far: 11.19000 # loops : 120 mean,max change (kT/e) : 4.5557137E-04 1.7490387E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.40000 DelPhi exited at 15:11:12 11.409u 0.458s 0:12.19 97.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 15:11:12 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5362 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.323524 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -16.08500 52.86200 ymin,ymax (A): 98.54200 167.0460 zmin,zma (A): -29.86400 31.83100 x,y,z range (A): 68.94701 68.50401 61.69500 scale (grids/A): 2.323524 object centre (A): 18.38850 132.7940 0.9835005 number of atom coordinates read : 5362 total number of charged atoms : 5190 net assigned charge : -5.499956 assigned positive charge : 818.3576 centred at (gu) : 86.83767 83.35506 81.68634 assigned negative charge : -823.8639 centred at (gu) : 86.75243 83.75227 81.41835 start vw surface at 0.2600000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 235568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42537 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 105757 mr = 176133 m= 26982 mr = 84264 m= 3749 mr = 20035 m= 202 mr = 2337 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 1.510000 no. cavity mid-points inaccessible to solvent = 11632 time to turn everything in is 2.500000 number of dielectric boundary points 89433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 2.670000 number of grid points assigned charge 41419 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.549016 object centre at (A) : 18.38850 132.7940 0.9835005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8407072E-02 -0.1413625 midg,1,midg; midg,igrid,midg 0.4516371 -0.2240576 1,midg,midg; igrid,midg,midg -0.2845162 -8.9581115E-03 gauss-seidel spectral radius is 0.9991831 estimated iterations to convergence 276 setup time was (sec) 2.870000 now iterating at: 15:11:15 rms-change max change #iterations 11.18948 278.9049 at 10iterations 6.428292 159.8975 at 20iterations 3.660553 88.71672 at 30iterations 2.072468 43.34649 at 40iterations 1.172718 24.47863 at 50iterations 0.6608612 13.23479 at 60iterations 0.3723055 7.259262 at 70iterations 0.2091397 3.561638 at 80iterations 0.1170078 2.074611 at 90iterations 6.5681383E-02 1.141283 at 100iterations 3.6833774E-02 0.6554489 at 110iterations 2.0662969E-02 0.3742890 at 120iterations 1.1565285E-02 0.1968784 at 130iterations 6.5068258E-03 0.1113367 at 140iterations 3.6648586E-03 6.4907074E-02 at 150iterations 2.0714325E-03 3.7036896E-02 at 160iterations 1.1816275E-03 2.3353577E-02 at 170iterations 6.8077788E-04 1.2485504E-02 at 180iterations finished qdiffx linear iterations at : 15:11:32 total time elapsed so far: 19.35000 # loops : 180 mean,max change (kT/e) : 6.8077788E-04 1.2485504E-02 energy calculations done at 19.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.57000 DelPhi exited at 15:11:32 19.574u 0.482s 0:20.35 98.5% 0+0k 0+0io 0pf+0w